AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons024_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245147
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH1	170	conserved protein
#1	MTH5	22	ribosomal protein L8 (E.coli L2)
#2	MTH9	46	ribosomal protein L35 (E.coli L29)
#3	MTH21	109	ribosomal protein L19
#4	MTH31	30	ribosomal protein L14
#5	MTH34	236	ribosomal protein S18 (E.coli S13)
#6	MTH40	58	DNA-dependent RNA polymerase, subunit N
#7	MTH42	171	DNA-dependent RNA polymerase, subunit K 
#8	MTH43	51	enolase
#9	MTH44	27	ribosomal protein Sa (E.coli S2)
#10	MTH47	21	conserved protein
#11	MTH48	73	conserved protein
#12	MTH684	42	conserved protein
#13	MTH686	65	proteasome, alpha subunit
#14	MTH689	74	conserved protein
#15	MTH690	170	ribosomal protein L15
#16	MTH691	115	conserved protein
#17	MTH1201	95	conserved protein
#18	MTH1202	236	proteasome, beta subunit
#19	MTH1203	69	cleavage and polyadenylation specificity factor

Motif 1
          CCTCACCAGCGGAAAGTTTAA	0	0	1
GAAAATATGCCCCTTCCAGTCCTCC      	3	4	0
GGCATATTTTCCAGTCCAGCGAAAAAACTTT	3	24	1
TATGATACATCCTGTGCCGGGATAGCCTAGC	5	56	1
CAGTCTTGCGCCTTACCTGGCTAGGCTATCC	5	75	0
CACAAGATTTCCAGTCTTGCGCCTTACCTGG	5	86	0
TGGAGCTTTGCTCCTCCTGGGTTCAAATCCC	5	115	1
GGTTCAAATCCCAGTCCCGGCGTCGGTTAAA	5	134	1
TTCGCAAACCCCCGTCCCGCGAATTCACTCT	5	199	1
CTCCAGCGTTCCGGTGCTGACCATCCCCGTT	7	75	0
CTGTAAAGCACCAGATCAGGGCTC       	16	101	1
TGGGGACAGCCCTTTGCAGGGTTAAATGAAA	18	143	1
TAATAAAAAACCAGTCCTGGATCCCATTGTG	18	195	0
          ** ********
MAP Score: 13.3621

Motif 2
GTCCAGCGAAAAAACTTTTTAAGGGGATACCTGAAA	3	37	1
   TCAAGAAACCTCCTTGTATTCAGCATTTGCTGA	3	86	0
GTATATTATGACATCTATTTAAGTATTGCTGCCGTC	5	15	0
GAATCCAAGAACCTCTATTTTAATGTTTTTCTTGGA	7	140	1
ACTCTAATAAACCACTATTTTTCAGTCTAGAGTTTA	8	10	1
   TTTTCTAACCTCTCTTTATTGATGGATAATTTA	13	42	0
CAGCCCCTTTACCCCTGTTTCGGAGGCCCCTGTTCT	14	11	0
TAGCACCTAAACCGCTATTTTTCAGGGATACGTTCC	15	105	1
TTTAATAAGGACCTCCTGTTATATATTGGTACAGAA	18	95	1
GTCCATGGGGACAGCCCTTTGCAGGGTTAAATGAAA	18	138	1
ATTGCAGTAAACACCTGTTTACTGATATTCCCTGTT	19	27	1
          *** ** ***    **
MAP Score: 12.2733

Motif 3
AGCACCTAAACCGCTATTTTTCAGGGATACGTTCCCAT	15	106	1
CTTTTTTCCTCCAAGTATTTAATGGCTTTTACGGAAGA	17	50	1
GTCCATGGGGACAGCCCTTTGCAGGGTTAAATGAAAAC	18	138	1
AATCCAAGAACCTCTATTTTAATGTTTTTCTTGGAGGC	7	141	1
AAGGGGATACCTGAAATTTTTCGGGTTTATCAGCAAAT	3	57	1
GTTATGCCTCCCTGTTTTTTGAAGGCTAAAAGGAGAGG	12	14	0
CTCTAATAAACCACTATTTTTCAGTCTAGAGTTTATTA	8	11	1
CGTTTATTCTCCTTACCTTTTCTGTAAAAAGGCGCTAT	16	35	1
AGCAAAGCTCCACAAGATTTCCAGTCTTGCGCCTTACC	5	89	0
GAACGGTTATCCGGTCATTAAAAGGAATGAGGTGGGAG	18	12	0
ATTTTTAATTACATTTTTTTGCCGTTTATTCTCCTTAC	16	13	1
CCTGGATCCCATTGTGTTTTTATGGTATATAAAGGGTT	18	173	0
GTCCAGCGAAAAAACTTTTTAAGGGGATACCTGAAATT	3	37	1
CGCTATATTTATCATCCTTTAATGTGTTTATTCTCTGT	16	67	1
ATTGCAGTAAACACCTGTTTACTGATATTCCCTGTTTT	19	27	1
    ATATTGAAACTTATTTGAGGTGATAGA       	9	6	1
CTGATATTCCCTGTTTTTTAGAAGTGATCTT       	19	48	1
GAGCCCTGATCTGGTGCTTTACAGAGAATAAACACATT	16	87	0
          **     *** * ** **
MAP Score: 10.7065

Motif 4
  CCGAATATCCTCCTGGTTATTT         	1	1	0
  TCAAGAAACCTCCTTGTATTCAGCATTTGCT	3	88	0
   TAAATCACCTCAGTAACTTTTAGTATGATG	4	10	0
CTTGGTCCATCCTCCCAGCCATTGAAGAAGTTT	7	25	1
         TCCTCCTCTCCTTTTAGCCTTCAA	12	1	1
    GTTATGCCTCCCTGTTTTTTGAAGGCTAA	12	23	0
TATCTTACCTTCTCAGCCCCTTTACCCCTGTTT	14	27	0
TGCCGTTTATTCTCCTTACCTTTTCTGTAAAAA	16	32	1
GTTCTTTTTTCCTCCAAGTATTTAATGGCTTTT	17	47	1
  TACTCCCACCTCATTCCTTTTAATGACCGGA	18	8	1
TTAATAAGGACCTCCTGTTATATATTGGTACAG	18	96	1
      TTTTTCTCCTATTTTTAATTGCAGTAA	19	4	1
          *****   *****
MAP Score: 10.6379

Motif 5
AGCGAAAAAACTTTTTAAGGGGATACCTGA	3	41	1
ATTATGACATCTATTTAAGTATTGCTGCCG	5	17	0
AACTTTATATATTTTTATTTTATAAACTAA	6	20	1
AAGAACCTCTATTTTAATGTTTTTCTTGGA	7	146	1
ATAAACCACTATTTTTCAGTCTAGAGTTTA	8	16	1
CCTATAAATTCCTTTGAATGTTGATTGATA	11	23	0
GTGATGGAAAATTTTTAAGGGCGTTAAAAT	11	53	1
   AACAACACCTTTGATTTTTCCATTAAA	15	7	1
TGACAGTAAACTTTTTAAGTGATCACACCA	15	68	1
CTAAACCGCTATTTTTCAGGGATACGTTCC	15	111	1
       TTCATTTTTAATTACATTTTTTT	16	3	1
ATTCTCCTTACCTTTTCTGTAAAAAGGCGC	16	40	1
TATTTATCATCCTTTAATGTGTTTATTCTC	16	72	1
CCACCTCATTCCTTTTAATGACCGGATAAC	18	15	1
TTGGTACAGAACTTTTATGTCCATGGGGAC	18	120	1
TGGGGACAGCCCTTTGCAGGGTTAAATGAA	18	143	1
TTTTTCTCCTATTTTTAATTGCAGTAAACA	19	10	1
          **********
MAP Score: 9.81589

Motif 6
GAGCATACAATGTGAGCGGATCCACCGCAGATTG	0	64	0
 CTATTAATATCTGTCCGGATTTATTTATAAATA	0	147	0
GAAAAAACTTTTTAAGGGGATACCTGAAATTTTT	3	44	1
ACTAAAAGTTACTGAGGTGATTTA          	4	16	1
TGATACATCCTGTGCCGGGATAGCCTAGCCAGGT	5	58	1
TTGGATTCGATTTGATGGGACCGCCGAGATTTGA	7	114	0
TAGAGTTTATTATGAGGTGTTTTA          	8	37	1
TTGAAACTTATTTGAGGTGATAGA          	9	13	1
CAAAGGAATTTATAGGGTGATGGAAAATTTTTAA	11	37	1
CTGACATTTCATTGATGTGACTGACAGTAAACTT	15	47	1
TGCTACTACATCTGGTGTGATCACTTAAAAAGTT	15	76	0
CATTCCTTTTAATGACCGGATAACCGTTCTTCAA	18	21	1
GATGGGGCTTCCTGAGGGGTTGAAGAACGGTTAT	18	40	0
GGGACAGCCCTTTGCAGGGTTAAATGAAAACCCT	18	145	1
TTTTATGGTATATAAAGGGTTTTCATTTAACCCT	18	160	0
          * *** *****  *
MAP Score: 8.62547

Motif 7
CATTGTATGCTCTGATACGATGTGGTCTGTGGTT	0	86	1
GCGAATTCACTCTTACTGGAGGTTAATGA     	5	217	1
GGTTCTTGGATTCGATTTGATGGGACCGCCGAGA	7	119	0
AAGAAAAACATTAAAATAGAGGTTCTTGGATTCG	7	139	0
CAGTCTAGAGTTTATTATGAGGTGTTTTA     	8	32	1
  ATATTGAAACTTATTTGAGGTGATAGA     	9	8	1
CTTCACTGACATTTCATTGATGTGACTGACAGTA	15	42	1
CAGGGATACGTTCCCATGGATGTGGCGTAAAGCC	15	127	1
GTAAAGCCGAACAGAATAGAGGTGTAA       	15	153	1
TGCGATTTTTTTATAATAGATGGGGCTTCCTGAG	18	58	0
TTTTTATTATTTTTATTAGAGGTGTATCT     	18	217	1
          **  * * ******
MAP Score: 8.00318

Motif 8
GCGGAAAGTTTAAATATGGATACCATACAATTTT	0	18	1
GAGCATACAATGTGAGCGGATCCACCGCAGATTG	0	64	0
TATTTATAAATAAATCCGGACAGATATTAATAG 	0	147	1
          TATATATGGACAGATTCATATCAG	2	0	1
CAGTGAATAATAGAAAGGGATTGAA         	2	31	1
GAAAAAACTTTTTAAGGGGATACCTGAAATTTTT	3	44	1
TGATACATCCTGTGCCGGGATAGCCTAGCCAGGT	5	58	1
TTGGATTCGATTTGATGGGACCGCCGAGATTTGA	7	114	0
TTGAAACTTATTTGAGGTGATAGA          	9	13	1
GCCACATCCATGGGAACGTATCCCTGAAAAATAG	15	119	0
CCTCCTGTTATATATTGGTACAGAACTTTTATGT	18	106	1
AACTTTTATGTCCATGGGGACAGCCCTTTGCAGG	18	129	1
ACCATAAAAACACAATGGGATCCAGGACTGGTTT	18	185	1
          *  *  ********
MAP Score: 2.1158

Motif 9
ATATGCCCCTTCCAGTCCTCC          	3	0	0
CCGAAAAATTTCAGGTATCCCCTTAAAAAGT	3	50	0
          TCAAGAAACCTCCTTGTATTC	3	98	0
CGGCGTCGGTTAAAGCAACCCTGTTGCACCT	5	151	1
GGTAGCTTGGTCCATCCTCCCAGCCATTGAA	7	20	1
AACTCGGGTCTCCAGCGTTCCGGTGCTGACC	7	84	0
TTAAAAATTTTCCATCACCCTATAAATTCCT	11	40	0
         GTTATGCCTCCCTGTTTTTTGA	12	30	0
TTACCCCTGTTTCGGAGGCCCCTGTTCTT  	14	8	0
GAAGGTAAGATAAAGCCCCCCGTCTTAACTT	14	48	1
CGGATAACCGTTCTTCAACCCCTCAGGAAGC	18	37	1
CTTCAACCCCTCAGGAAGCCCCATCTATTAT	18	49	1
TAAAGGGTTTTCATTTAACCCTGCAAAGGGC	18	151	0
AAAAAACCAGTCCTGGATCCCATTGTGTTTT	18	191	0
          ******* ***
MAP Score: 1.42621

Motif 10
TTCTATTATTCACTGATATGAATCTGTCCA	2	16	0
 GTTATGCCTCCCTGTTTTTTGAAGGCTAA	12	23	0
TTTCGGAGGCCCCTGTTCTT          	14	0	0
GCCCCTTTACCCCTGTTTCGGAGGCCCCTG	14	15	0
CCCCCGTCTTAACTTTTTTT          	14	64	1
TATTCTCCTTACCTTTTCTGTAAAAAGGCG	16	39	1
       GAGCCCTGATCTGGTGCTTTACA	16	102	0
ATAAATCCATAAGTGTTCTTTTTTCCTCCA	17	33	1
ATTGGTACAGAACTTTTATGTCCATGGGGA	18	119	1
TACTGATATTCCCTGTTTTTTAGAAGTGAT	19	46	1
TGTTTTTTAGAAGTGATCTT          	19	59	1
          **********
MAP Score: 0.867663